Here is some additional information on the CRAM file format if anyone would like to better familiarize themselves: https://academic.oup.com/bioinformatics/article/38/6/1497/6499262

Added cram to IGB supported file format. See commit

Karthik Raveendran - how do we want to tackle version checking for cram?

Option 1: Do nothing, any user who is using an older version of IGB will see the View in IGB button for a CRAM file, but when clicked it will throw an error in IGB.
Option 2: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will not show the View in IGB button for CRAM files.
Option 3: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will show a modal informing the user "To view a CRAM file in IGB, please update your IGB to the most recent version".

I think we are checking IGB version in cyverse.js and there is a popup_modals.html warning for older versions of IGB.

Implemented Option 3 from the prev comment by Dr. Nowlan Freese. See commit

PR Submitted. https://bitbucket.org/nfreese/bioviz-connect/pull-requests/291

To deploy testing and new versions using code in bioviz connect playbooks repository.

AL request: Karthik Raveendran to take over deploying new versions of bioviz connect code, using playbooks.

Merged and deployed to connect.bioviz.org/

Deployed following instructions from bioviz-connect-playbooks repo with:

ansible-playbook -i inventory.ini setup.yml

Once the playbook was completed I had to hit the SyncAppDataToBioViz endpoint to see the change:

https://connect.bioviz.org/SyncAppDataToBioViz/?accesstoken=<validKeyCloakAccessToken>

I first tested the changes on bvctest7 (Nowlan has access to start/stop the instance).

Note that you will need to proper crt files and key. You will also need to have a properly filled out inventory.ini and group_vars > setup_vars.yml files. I also specify my repo in the roles > clone > defaults > main.yml file:

repo: https://bitbucket.org/nfreese/bioviz-connect.git

I uploaded a folder with matching cram/bam/sam files. I was able to modify the metadata to specify the Arabidopsis genome for the CRAM file. Once the CRAM file and its index were made public I was able to click View in IGB and view the files in IGB. If I tried to load a CRAM file into a version of IGB less than 10.0.0 I saw a warning from BioViz Connect that I should upgrade my version of IGB.

Closing ticket.